The great crystal of Atlantis was hidden beneath the city by Kida's father; the crystal is living and keeps Atlantis and its people alive. The crystal grew a conscience when Kida's father tried to use the crystal's power as a weapon and that's what caused Atlantis to sink. Milo and the crew rescue Kida from Rourke. Kida, fused with the crystal, saves the city from being destroyed by lava. Audrey, Mole, Vinny, Sweet, Mrs. Packard and Cookie return to the U.S. with a few treasures. They provide to Mr. Whitmore evidence that they reached Atlantis; Milo sends him a crystal and a thank you note for believing in him and his grandfather. Milo stays in Atlantis and Kida is the next to rule Atlantis. Instead of having the great crystal beneath the city, it's now above the city and the Atlantean civilization is no longer in danger of dying.

In the beginning scenes, where Milo Thatch is practicing his proposal, he slides over (face forward, chest against the board) a chalk drawing of a map detailing the location of Atlantis. When he realises he wiped off the drawing, and sees it on his clothes, he stands in front of the blank part of the chalkboard, "filling in" the space with the map that rubbed off on his shirt - the only problem is, that the image should have rubbed off backwards as he was facing the board when it transferred to his clothes. He could not simply stand in the place of the missing map face forward and have it read properly.

During the sequence with the explorers' huge submarine submerging, one of the computerized "extras" can be seen waving at the camera. (He is seen through the lower window for only a second or two; use frame advance to view it or listen to the Visual Commentary on the DVD for specifics).